Hello, Part of my Galaxy Workflow is to have Trimmomatic trim a FASTQsanger and to convert the output into a FASTQ.gz. Somewhere in the process, Trimmomatic gives the error pasted below. Does anyone know what this means? Is it not able to compress the output into fastq.gz?
Thanks,
Dan
Fatal error: Exit code 1 () Trimmomatic did not finish successfully The tool produced the following additional output: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/015/675/15675107/_galaxy_tmp -Xmx7680m -Xms256m TrimmomaticSE: Started with arguments: -threads 1 -phred33 fastq_in.fastq.gz fastq_out.fastq.gz SLIDINGWINDOW:4:20 Exception in thread "main" java.util.zip.ZipException: Not in GZIP format at java.util.zip.GZIPInputStream.readHeader(Unknown Source) at java.util.zip.GZIPInputStream.<init>(Unknown Source) at java.util.zip.GZIPInputStream.<init>(Unknown Source) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:100) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:96) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.nextGzipInputStream(ConcatGZIPInputStream.java:38) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.<init>(ConcatGZIPInputStream.java:16) at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:140) at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:197) at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:306)
This might be a case where the input was labeled as fastq.gz when it actually was simply fastq. Mismatches between the datatype and actual dataset content is problematic.
See the help here, make corrections if needed, rerun, and let us know what happened. If there is another error, we might ask you to send in a bug report.
Thanks, Jen, Galaxy team
Hi Jen, As usual, thank you for your prompt reply. I read the information in the links you attached and curated all files names and attributes but the outcome was still the same (see error below). I think either there is something else that I'm doing wrong (and usually algorithms do not run if you don't provide them with proper input format) or Trimmomatic is being moody... Any help would be much appreciated! Thanks, Dan
Dataset generation errors Dataset 1: trimmedFastqSangerGZ
Tool execution generated the following error message: Fatal error: Exit code 1 () Trimmomatic did not finish successfully The tool produced the following additional output: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/015/678/15678452/_galaxy_tmp -Xmx7680m -Xms256m TrimmomaticSE: Started with arguments: -threads 1 -phred33 fastq_in.fastqsanger.gz fastq_out.fastqsanger.gz SLIDINGWINDOW:4:20 Exception in thread "main" java.util.zip.ZipException: Not in GZIP format at java.util.zip.GZIPInputStream.readHeader(Unknown Source) at java.util.zip.GZIPInputStream.<init>(Unknown Source) at java.util.zip.GZIPInputStream.<init>(Unknown Source) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:100) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream$GZIPHelperInputStream.<init>(ConcatGZIPInputStream.java:96) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.nextGzipInputStream(ConcatGZIPInputStream.java:38) at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.<init>(ConcatGZIPInputStream.java:16) at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:140) at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:197) at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:306)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)